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• An Uncanny Family Resemblance to someone Alice or Bob knows.
• Alice and Bob are long lost relations of some sort.
• Alice or Bob is an Identical Stranger to someone.
• Alice or Bob is making an Actor Allusion, or part of a Casting Gag where they played characters who had a relationship in a different show, and the writers wanted to point that out.
• Alice or Bob knew each other in a past life.
• Alice or Bob is actually Christie or Charlie in a Paper-Thin Disguise.
• Alice or Bob is a Forgotten Childhood Friend.
• Alice or Bob is suffering from Cloning Blues.
• Alice or Bob simply has a bad memory, or more dramatically, is suffering from some kind of memory-related ailment.
• Alice or Bob do know each other, but one or the other is teasing.
  • Alternately, neither Alice nor Bob actually know each other; one of them is just being a flirt.
• Alice or Bob is Literal-Minded or a Cloudcuckoolander and misconstrued an otherwise innocuous statement. (See also Sarcasm Failure.)
• Alice or Bob is playing with the Timey Wimey Ball and suffering from a bit of Time Travel Tense Trouble, resulting in Have We Met Yet?.
• Alice or Bob has gone dimension-hopping and met Earth-1 Alice/Bob.
• Alice is actually Alex (or Bob is actually Barbara).
• Alice and Bob do know each other, and one of them is asking the other "What are you doing here?" in a way that does not tip off the others to their association.
• Alice and Bob do know each other, but Alice considers Bob an Abhorrent Admirer (or vice versa).

Examples:

• At the end of Rurouni Kenshin, Enishi and his father, whom we only know as "oibore", run into each other in the hobo camp and have the vaguest feeling that they may know each other, but neither thinks anything of it (or oibore just decided to not reveal himself).
• In a chapter of Ranma ½, Akane gets brainwashed (literally, with shampoo on the scalp) to forget Ranma. She says this to Ranma multiple times in the chapter, but also once to her dad as a joke.
• In the first episode of Martian Successor Nadesico Yurika runs into Akito and asks if she's met him before. Akito says that they've never met, not realizing until Yurika has left that she's the girl he was friends with as a child.
• Haruhi Suzumiya asks Kyon this during their first conversation. She has in fact met him before, but Kyon hasn't; he will meet her three years ago a couple of months later.

• Duck Soup
  Ambassador Trentino: Have we met each other before, sir?
  Rufus T. Firefly: I don't think so. In fact, I'm not sure I'm seeing you now; it must be something I ate.
• Get Shorty
  Harry Zimm: Have we met? I don't recall.
  Chili Palmer: We just did. I told you, my name is Chili Palmer.
• Multiplicity. Doug Kinney has been suffering from Cloning Blues.
  Woman in Restaurant: Have we met?
  Doug Kinney: No.
• Tarzan: Clayton says it after hearing Tarzan say his name, which he learned from Jane. Later, he uses it more sarcastically when Tarzan is captured by his minions.
• Pirates of the Caribbean
  Captain Jack Sparrow: You look somewhat familiar, have I threatened you before?
• Dr. Horrible's Sing-Along Blog
  Cpt. Hammer: You look horribly familiar.
• Doubles as a Tear Jerker in Deja Vu when Claire, who just witnessed her rescuer, Doug, get killed in an explosion, sees his present-day self (as opposed to the one who traveled back in time and was killed) appear. He then asks her this question when she is on the verge of tears at seeing him.
  • Becomes a Crowning Moment of Heartwarming when Doug seems to regain his future self's memories of Claire at the end of the movie.

• Alias episode "Succession"
  Ushek San'ko: Chateau Patreuse, 1982...your favorite, no?
  Julian Sark: [surprised] Have we met?
• Arrested Development episode "Forget Me Now"
  Larry: Interfere? I ought to pull down your pants and spank your ass raw.
  Michael: I'm sorry, have we met?
• Buffy the Vampire Slayer "Becoming: Part 2"
  Joyce: Have we met?
  Spike: Uh, you hit me with an axe one time. Remember "Get the hell away from my daughter"?
• Charlie's Angels episode "To See an Angel Die"
  Kris Munroe: Have we met?
  Tom Grainger: No, we've never met. But we have something in common.
  Kris Munroe: Oh?
  Tom Grainger: My name is Tom Grainger. You killed my wife. [Prepare to Die]
• Star Trek: Deep Space Nine episode "Emissary"
  Commander Benjamin Sisko: It's been a long time, Captain.
  Captain Jean-Luc Picard: Have we met before?
  Commander Sisko: Yes, sir. We met in battle. I was on the Saratoga at Wolf 359*

  Where his wife was killed by the Borg cube commanded by Locutus (Picard)

  .
• The Six Million Dollar Man "The Bionic Woman: Part 2"
  Joseph Ronaugh: Colonel Steven Austin. I can't tell you what a pleasure it is to see you face to face again.
  Col. Steve Austin: Have we met before?
• Subverted famously in Seinfeld, such as in this example:

  George, into the phone: Jerry! Jerry, you gotta help me!

  Jerry: * Pauses, smiling* Who is this?

• Misfits S1E4, after Curtis rewound time so that he never got his ASBO. Happens repeatedly, even! With the same character, too!
  Curtis: Oy, Nathan, I need your help!
  Nathan: ...Do I know you? [glances at Curtis, who is kneeling] Are you taking a shit? There's a guy over here taking a shit!
  Curtis: I'm not taking a shit!
  Nathan: How do I know you again?
  • And then again:
  Curtis: [later, after rewinding time again] It's you!
  Nathan: What? Do I know you?

• One especially lovely Mel Tormé song, about setting up a meeting with an old flame, is called Haven't We Met?

• Final Fantasy IX
  Lani: I've been looking for you, Princess Garnet.
  Zidane: Have we met?
  Garnet: Quit flirting with her!
• An almost Tear Jerker example in Kingdom Hearts II when Sora meets the real versions of the kids that were Roxas' friends in the Twilight Town simulation.
• In Oblivion, in the town Chorrol some people make remarks about how they met one of the inhabitants in a totally different town, and he acted as if he had never met them. When you investigate this, it turns out the person in question proves to be the long lost, assumed dead, other half of an identical twin.
• In Super Robot Wars Original Generation, Masaki asks Gilliam if they know each other. Gilliam assures them that they don't, although he knows the Masakis from the Hero Senki and Classic Super Robot Wars timelines.
• In The Legend of Zelda: Majora's Mask, Anju is supposed to be getting married to Kafei the day after the 3rd day, but the Skull Kid turned Kafei into a child. If you do everything necessary to get the good ending to their sidequest, Kafei meets with her, still appearing as a child. Anju remembers having met him before.

• In Misfile, during the wedding, Heather says this to Ash after (s)he introduces her to his/her friends. Apparently, Ash being a girl means that they never met.
• In The Inexplicable Adventures of Bob!, Galatea is confused when Riboflavin mistakes her for Molly.

• American Dad! episode "Finances with Wolves"
  Francine Smith: You know, you seem very familiar. Have we met before?
  Klaus: Oh, you know, I'm just one of those black Germans that seems familiar to everyone, hmm?
• Avatar The Last Airbender Suki is out of her uniform and full face makeup, and Sokka doesn't recognize her. She decides to play this up for a good laugh.
  Sokka: Is there a problem?
  Female Security Guard: Yeah, I got a problem with you. I've seen your type before. Probably sarcastic, think you're hilarious. And let me guess, you're traveling with the Avatar.
  Sokka: Do I know you?
  Guard: You mean you don't remember? Maybe you remember this. (kisses him)
  Sokka: Suki!
  • Subverted in a later episode when Sokka attempts a similar stunt while disguised as a helmeted Fire Nation prison guard, and Suki clocks him one before she recognizes him.
• In one episode of Gargoyles, Owen Burnett is asked this question by another, identical-but-for-hair-color majordomo named Preston Vogel, and Owen replies, "I assure you, we have not." This is not a case of Only Six Faces, though, since Puck deliberately chose the man as his inspiration for his Owen alter ego.
• Spider-Man Unlimited
  Spider-Man: Electro?
  Lester: Have we met?
  Spider-Man: Sorta, but the Electro I know looks like a movie star.
• The Batman episode "Call of the Cobblepot"
  The Penguin: Bruce Wayne! King of the castle, ruler of the roost.
  Bruce Wayne: Have we met?
  The Penguin: Cobblepot. Oswald Cobblepot.